Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Pathway-targeting gene matrix for Drosophila gene set enrichment analysis.

  PMID 34710184 · PMC8553153 · PloS one · 2021 · 8 claims · 4 setups

  Has reproduction · 95

  Gene matrix files for GSEA are largely unavailable for Drosophila, limiting pathway-level enrichment analysis in this model organism

  drosophila reactome kegg gene fluorescence manual

• De novo identification of CD4(+) T cell epitopes.

  PMID 38658646 · PMC11093748 · Nature methods · 2024 · 7 claims · 8 setups

  Has reproduction · 83

  SABR-IIs (chimeric receptors linking a covalently attached peptide-MHC-II to CD28-CD3ζ signaling domains) present epitopes to CD4+ T cells and induce a readable NFAT-GFP/CD69 signal upon cognate TCR recognition

  nfat-gfp hla-dq8 5kc daudi nfat-gfp co-incubation species

• Genetically engineered stem cell-derived retinal grafts for improved retinal reconstruction after transplantation.

  PMID 34409267 · PMC8361135 · iScience · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  Bhlhb4−/− and Islet1−/− pluripotent cell lines differentiate into retinal organoids with similar timing, morphology, and gene expression to wt lines up to around DD15

  bhlhb4− nrl-gfp rd1 fluorescence rt-pcr microarray

• A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport.

  PMID 33649340 · PMC7921559 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 96

  A total of eight human mRNAs (PCNT, NIN, BICD2, CCDC88C, CEP350, HMMR, ASPM, NUMA1) localize at centrosomes.

  hela hela–centrin1–gfp drosophila high-throughput low-throughput smfish

• Cancer-cell-secreted miR-204-5p induces leptin signalling pathway in white adipose tissue to promote cancer-associated cachexia.

  PMID 37620316 · PMC10449837 · Nature communications · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  Breast cancer cell-secreted exosomal miR-204-5p induces HIF1A in white adipose tissue by targeting the VHL gene.

  balb nsg ewat iwat orthotopic indirect sev

• Differential bone morphology and hypoxia activity in skeletal metastases of ER(+) and ER(-) breast cancer.

  PMID 39572705 · PMC11582807 · Communications biology · 2024 · 8 claims · 8 setups

  Has reproduction · 68

  ER− MDA-MB-231 breast cancer forms more osteolytic bone metastases than ER+ MCF-7 breast cancer

  mcf-7 breast bone tumor-free immunofluorescence co-culture rna-seq

• Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.

  PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups

  Has reproduction · 68

  A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.

  hek293 coli dual genome-wide western

• Antigen and checkpoint receptor engagement recalibrates T cell receptor signal strength.

  PMID 34534438 · PMC8585507 · Immunity · 2021 · 8 claims · 6 setups

  Has reproduction · 37

  TCR signal strength drives dynamic and time-dependent transcriptional changes in CD4+ T cells in vivo

  tg4 splenic sorted flow bulk checkpoint

• Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.

  PMID 16179648 · PMC1236720 · Nucleic acids research · 2005 · 8 claims · 4 setups

  Full-text index only

  Deeply conserved human-zebrafish non-coding elements are enriched for in vivo cis-acting transcriptional regulatory activity.

  ncbi genes zebrafish comparative annotation gfp

• Distinct sympathetic projections to brown fat regulate thermogenesis and glucose tolerance.

  PMID 41559445 · PMC12945688 · Nature metabolism · 2026 · 8 claims · 8 setups

  Has reproduction · 85

  Distinct sympathetic neuron subpopulations in the stellate ganglion (SG) innervating iBAT parenchyma versus its vasculature mediate separable functions of the depot.

  th-cre awake ibat plasma retrograde chemogenetic indirect

• Spatially resolved phosphoproteomics reveals fibroblast growth factor receptor recycling-driven regulation of autophagy and survival.

  PMID 36329028 · PMC9633600 · Nature communications · 2022 · 8 claims · 6 setups

  Has reproduction · 87

  A spatially resolved phosphoproteomics (SRP) approach combining APEX2-driven proximity biotinylation with phosphopeptide enrichment was developed to identify FGFR2b signalling partners near recycling endosomes.

  hela_fgfr2bst hela-fgfr2b hela_fgfr2b-apex2st hela-fgfr2bst_rab11-apex2 confocal western ms-based

• Recruitment of the m(6)A/m6Am demethylase FTO to target RNAs by the telomeric zinc finger protein ZBTB48.

  PMID 39300486 · PMC11414060 · Genome biology · 2024 · 8 claims · 8 setups

  Has reproduction · 78

  ZBTB48 physically interacts with the m6A/m6Am demethylase FTO

  hek293 inducible polyadenylated ap-ms co-immunoprecipitation clip

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

  cast inbred gfp mescs single-cell smfish flow

• Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development.

  PMID 34643182 · PMC8555986 · eLife · 2021 · 7 claims · 8 setups

  Has reproduction · 84

  Tbx5 directly maintains Aldh1a2 expression in the foregut lateral plate mesoderm via an evolutionarily conserved intronic enhancer

  e9.5 xenopus bulk rt-qpcr whole-mount

• Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.

  PMID 28446242 · PMC5406893 · Genome medicine · 2017 · 7 claims · 6 setups

  Has reproduction · 92

  Breast tumors exhibit two discrete GFRN activity phenotypes: a 'survival phenotype' with concordant HER2/IGF1R/AKT activation and a 'growth phenotype' with concordant EGFR/KRAS(G12V)/RAF1/BAD activation, which are typically mutually exclusive.

  mammary tcga hmecs breast rna-sequencing pathway western

• Reactive astrocytes acquire neuroprotective as well as deleterious signatures in response to Tau and Aß pathology.

  PMID 35013236 · PMC8748982 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  Aβ (APP/PS1) and Tau (MAPT P301S) pathology induce distinct but overlapping astrocyte translatome signatures

  astrocytes aldh1l1_egfp-rpl10a astrocyte ageing trap-seq immunofluorescence ribosome

• An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

  PMID 19012953 · PMC2990916 · Cell · 2008 · 7 claims · 8 setups

  Full-text index only

  shRNA pools targeting genes recurrently deleted in human HCC accelerate hepatocarcinogenesis in vivo, whereas randomly selected shRNA pools do not.

  hepatocellular p53 genomic hepatoma array-based pooled shrna

• Identification of new ETV6 modulators through a high-throughput functional screening.

  PMID 35198911 · PMC8851229 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 68

  A genome-wide shRNA screen in an engineered ETV6-dependent Blasticidin-sensitive pre-B ALL cell line can identify modulators of ETV6 repressive transcriptional activity

  reh genome-wide qrt-pcr chip-seq

• The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.

  PMID 21857667 · PMC3173870 · Nature cell biology · 2011 · 8 claims · 8 setups

  Has reproduction · 90

  Brain tumors in l(3)mbt mutants originate from overproliferation of neuroepithelial cells of the optic lobes, not from defects in asymmetric cell division.

  drosophila chip-seq chip immunostaining

• Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics.

  PMID 12213833 · PMC2173151 · The Journal of cell biology · 2002 · 8 claims · 8 setups

  Full-text index only

  Subcellular proteomics of purified CCVs identifies enthoprotin (encoded by KIAA0171), a novel ENTH domain-containing protein not previously detected at the protein level.

  brain cos-7 hek-293 clathrin subcellular western ccv